Variant report

Variant	rs2276561
Chromosome Location	chr2:113956371-113956372
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113931492..113932996-chr2:113955583..113957836,2	MCF-7	breast:
2	chr2:113894199..113895178-chr2:113956349..113957482,7	MCF-7	breast:
3	chr2:113949542..113953586-chr2:113955251..113958622,5	MCF-7	breast:
4	chr2:113954862..113956783-chr2:113998620..114001129,2	MCF-7	breast:
5	chr2:113955248..113957880-chr2:113994557..113996875,2	MCF-7	breast:
6	chr2:113947298..113949233-chr2:113956219..113958532,2	MCF-7	breast:
7	chr2:61404133..61405069-chr2:113956037..113956958,2	HCT-116	colon:
8	chr2:113912322..113918193-chr2:113953978..113958305,10	MCF-7	breast:
9	chr2:113913769..113918338-chr2:113954843..113958220,11	MCF-7	breast:
10	chr2:113950663..113952350-chr2:113953925..113956890,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000173209	Chromatin interaction
ENSG00000125618	Chromatin interaction
ENSG00000234174	Chromatin interaction
ENSG00000125637	Chromatin interaction
ENSG00000189223	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10175462	0.82[ASN][1000 genomes]
rs10206269	0.81[ASN][1000 genomes]
rs1110839	0.81[ASN][1000 genomes]
rs11123170	0.82[ASN][1000 genomes]
rs11123172	0.82[ASN][1000 genomes]
rs12612729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12619508	0.84[EUR][1000 genomes]
rs12620738	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2015769	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2019137	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2241978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2305133	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2863243	0.82[ASN][1000 genomes]
rs3748916	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3811059	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3828188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3828189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4848318	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849169	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849176	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4849177	0.81[ASN][1000 genomes]
rs4849179	0.82[ASN][1000 genomes]
rs4849183	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62160781	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6707386	0.82[ASN][1000 genomes]
rs6755040	0.82[ASN][1000 genomes]
rs6755639	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs731834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7421852	0.81[ASN][1000 genomes]
rs7563094	0.82[ASN][1000 genomes]
rs7578633	0.82[ASN][1000 genomes]
rs895412	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs902695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs902696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv582711	chr2:113895516-113984503	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv582712	chr2:113932431-113985170	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv874899	chr2:113935407-113962071	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv874900	chr2:113948378-113967990	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2276561	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs2276561	AC016683.6	cis	lung	GTEx
rs2276561	AC016683.6	cis	Artery Tibial	GTEx
rs2276561	AC016683.6	cis	Whole Blood	GTEx
rs2276561	AC016683.6	cis	Muscle Skeletal	GTEx
rs2276561	PAX8	cis	Esophagus Muscularis	GTEx
rs2276561	PAX8	cis	Adipose Subcutaneous	GTEx
rs2276561	AC016683.6	cis	Nerve Tibial	GTEx
rs2276561	PAX8	cis	Esophagus Mucosa	GTEx
rs2276561	PAX8	cis	lung	GTEx
rs2276561	AC016683.6	cis	Esophagus Muscularis	GTEx
rs2276561	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs2276561	AC016683.6	cis	Esophagus Mucosa	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113939400-113956400	Weak transcription	Small Intestine	intestine
2	chr2:113940000-113961000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr2:113942800-113956600	Strong transcription	Fetal Thymus	thymus
4	chr2:113942800-113961000	Strong transcription	Dnd41	blood
5	chr2:113947400-113961000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr2:113947800-113959600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
7	chr2:113947800-113960600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr2:113948600-113961000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr2:113949000-113961200	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr2:113950000-113961000	Strong transcription	Primary T cells from cord blood	blood
11	chr2:113951000-113956400	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr2:113952600-113957800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr2:113954000-113956400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:113954000-113957000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:113954400-113956400	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr2:113955200-113956400	ZNF genes & repeats	Thymus	Thymus
17	chr2:113955400-113956400	Genic enhancers	Spleen	Spleen
18	chr2:113955800-113956400	Flanking Bivalent TSS/Enh	HepG2	liver
19	chr2:113955800-113956600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr2:113955800-113957000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr2:113955800-113957200	Weak transcription	Primary B cells from cord blood	blood
22	chr2:113955800-113957600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr2:113955800-113958000	Weak transcription	K562	blood
24	chr2:113955800-113959200	Enhancers	Stomach Mucosa	stomach
25	chr2:113956000-113956400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:113956000-113956400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:113956000-113956400	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:113956000-113956400	Genic enhancers	Primary monocytes fromperipheralblood	blood
29	chr2:113956000-113956400	Genic enhancers	Primary B cells from peripheral blood	blood
30	chr2:113956000-113956400	Flanking Active TSS	Liver	Liver
31	chr2:113956000-113956600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
32	chr2:113956000-113956600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:113956000-113956600	Active TSS	HSMM	muscle
34	chr2:113956000-113956800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:113956000-113956800	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:113956000-113957000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr2:113956000-113957000	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr2:113956000-113957000	Active TSS	Brain Angular Gyrus	brain
39	chr2:113956000-113957000	Active TSS	Brain Anterior Caudate	brain
40	chr2:113956000-113957000	Active TSS	Duodenum Mucosa	Duodenum
41	chr2:113956000-113957000	Enhancers	Fetal Brain Male	brain
42	chr2:113956000-113957000	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr2:113956000-113957000	Active TSS	A549	lung
44	chr2:113956000-113957000	Active TSS	Hela-S3	cervix
45	chr2:113956000-113957200	Active TSS	H1 Cell Line	embryonic stem cell
46	chr2:113956000-113957200	Active TSS	H9 Cell Line	embryonic stem cell
47	chr2:113956000-113957200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr2:113956000-113957200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr2:113956000-113957200	Active TSS	Colonic Mucosa	Colon
50	chr2:113956000-113957200	Active TSS	Duodenum Smooth Muscle	Duodenum

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